Thanks Ben. If the newer FoxS versions have more robust algorithms to deal with overfitting then I would heartily recommend that Chimera developers would redirect to the Sali server, which runs up-to-date software. There is an option of launching FoxS locally so I guess there is no reason not to use the most up-to-date version, but this does require some effort on the part of the user to install the IMP suite and point to the executable. Notwithstanding, I think the ability to fit the SAXS curve directly from a model loaded in Chimera and produce a very nice publication-quality graph is super-helpful and easy. Regards, Eugene On 5 August 2015 at 02:20, Ben Webb <ben@salilab.org> wrote:
On 08/03/2015 10:51 AM, Eugene Valkov wrote:
Thanks for a quick response and for clarifying this a bit. However, I am still none the wiser as to why there is a discrepancy between the SAXS fits reported by the version Chimera uses and the FoxS from the IMP suite or the Sali lab webserver.
Dina would be the person to ask (since she wrote FoXS). Her contact details are on the FoXS website.
Chimera folks: I'm not sure why the version of FoXS you're using is so old (if it's really IMP 2.1, that was released in 2013). If possible, Chimera should just talk directly to the Sali lab FoXS webserver. If that's not practical, it should be straightforward to update your web service to use the latest IMP 2.5.0 release.
For the record, I think Chimera reports
the more accurate values as they are in rough agreement with those from another program, Crysol.
It's far more likely that you're seeing overfitting here. That was certainly an issue in older versions of FoXS, long since fixed at our end.
Ben -- ben@salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle